[gmx-users] Net charge neutrality during thermodynamic integration

Michael Shirts mrshirts at gmail.com
Sun Jun 15 10:26:32 CEST 2014

Try this talk posted on Alchemistry.org by Gabe Rocklin who has carefully
looked at this problem.


And the full paper:


On Sun, Jun 15, 2014 at 2:47 AM, Leandro Bortot <leandro.obt at gmail.com>

> Dear users,
>      I'm learning how to use the Thermodynamic Integration approach to
> calculate free energy differences. I have done some tutorials, including
> those available at www.alchemistry.org.
>      however, all tutorials I found use neutral ligands for the decoupling.
> Since I use cutoffs with PME and some of my ligands are charged, I wonder
> how should I treat the fact that at labda=1.0 the system net charge will be
> neutral and at lambda=0.0 it will be a non-zero integer value because the
> ligand charges has been set to zero.
>     should I decouple a counter-ion together with the ligand or should I
> let the charge be non neutral and apply some sort of corrections in the
> results?
>      If possible, could you provide some paper or tutorial in which this is
> done and explained? Although I could find some papers in which charged
> ligands are decoupled, no explanation was given about the net charge.
> best regards,
> Leandro.
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list